From these calcs, Flamethrower gives more damage. I tested them on a Mew, which has equal defensive stats. Emboar, at Level 50, has 143 Atk, which is why I used Level 50. The Level doesn't matter much here; I was aiming for your attack stat. Emboar's Special Attack reaches 120, so I added 12 EVs to make it 123, like your Emboar. Emboar's Flamethrower ends up doing a bit more due to the extra power it offers.

In conclusion, Flamethrower will do more. But I highly recommend that you use Fire Punch over Flamethrower, as Emboar's attack will increase quite fast due to its high base attack. Fire Punch also has more reliability.